Variant report

Variant	rs7127013
Chromosome Location	chr11:72999221-72999222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr11:72999201-72999593	GM12878	blood:	n/a	n/a
2	SPI1	chr11:72999216-72999632	GM12878	blood:	n/a	chr11:72999474-72999487 chr11:72999405-72999414 chr11:72999406-72999413 chr11:72999476-72999485 chr11:72999473-72999486
3	SPI1	chr11:72999055-72999944	GM12878	blood:	n/a	chr11:72999474-72999487 chr11:72999405-72999414 chr11:72999406-72999413 chr11:72999476-72999485 chr11:72999473-72999486
4	MTA3	chr11:72999016-73000035	GM12878	blood:	n/a	n/a
5	EP300	chr11:72999196-72999628	GM12878	blood:	n/a	chr11:72999451-72999460 chr11:72999475-72999489
6	RELA	chr11:72999171-73000956	GM12891	blood:	n/a	chr11:72999958-72999967 chr11:72999958-72999967
7	SPI1	chr11:72999162-72999796	HL-60	blood:	n/a	chr11:72999474-72999487 chr11:72999405-72999414 chr11:72999406-72999413 chr11:72999476-72999485 chr11:72999473-72999486
8	SPI1	chr11:72999219-72999667	HL-60	blood:	n/a	chr11:72999474-72999487 chr11:72999405-72999414 chr11:72999406-72999413 chr11:72999476-72999485 chr11:72999473-72999486
9	RCOR1	chr11:72998945-73000966	IMR90	lung:	n/a	n/a
10	IKZF1	chr11:72999216-72999541	GM12878	blood:	n/a	n/a
11	RELA	chr11:72999177-73000897	GM18505	blood:	n/a	chr11:72999958-72999967 chr11:72999958-72999967
12	RUNX3	chr11:72999189-73000865	GM12878	blood:	n/a	n/a
13	SPI1	chr11:72999196-72999713	GM12891	blood:	n/a	chr11:72999474-72999487 chr11:72999405-72999414 chr11:72999406-72999413 chr11:72999476-72999485 chr11:72999473-72999486

No.	Distal block	Cell Line	Cell type
1	chr11:72996918..72999897-chr11:73019036..73021814,2	MCF-7	breast:
2	chr11:72463586..72465161-chr11:72998103..73000277,2	MCF-7	breast:
3	chr11:72896543..72900928-chr11:72997023..72999571,3	MCF-7	breast:
4	chr11:72994379..72997208-chr11:72997669..73000273,2	K562	blood:
5	chr11:72993607..72995871-chr11:72997923..72999784,2	MCF-7	breast:

Variant related genes	Relation type
P2RY6	TF binding region
ENSG00000110237	Chromatin interaction
ENSG00000257038	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10898913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10898914	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10898915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235699	1.00[JPT][hapmap]
rs11235701	0.95[ASN][1000 genomes]
rs11235703	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11235705	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11235706	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11235707	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235708	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235709	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235710	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235711	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235713	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12276627	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12363628	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12787775	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12790447	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12790863	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12794405	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12801084	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12803970	1.00[ASW][hapmap]
rs12808111	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894075	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513476	1.00[ASN][1000 genomes]
rs34023835	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34385073	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35455220	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35963948	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432047	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6592518	1.00[YRI][hapmap]
rs67897720	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103650	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7106903	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7114877	0.95[ASN][1000 genomes]
rs7116594	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123808	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127179	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7925649	1.00[JPT][hapmap]
rs7930891	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882904	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988805	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832208	chr11:72876184-73091003	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv520665	chr11:72999221-73061856	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7127013	PAAF1	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72984600-73000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:72986200-72999800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:72995000-72999600	Weak transcription	NHEK	skin
4	chr11:72995000-72999800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:72995200-72999400	Weak transcription	HMEC	breast
6	chr11:72995200-72999600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:72995400-72999400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:72995400-72999600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr11:72995400-72999800	Weak transcription	Esophagus	oesophagus
10	chr11:72995600-72999600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:72995600-72999800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:72996400-73001000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr11:72997000-73003400	Enhancers	Fetal Intestine Large	intestine
14	chr11:72997200-73001000	Genic enhancers	Fetal Intestine Small	intestine
15	chr11:72997400-72999800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:72997600-72999400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:72997600-73000000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:72997600-73000200	Enhancers	K562	blood
19	chr11:72997800-72999800	Enhancers	A549	lung
20	chr11:72997800-73000200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:72997800-73000800	Enhancers	Lung	lung
22	chr11:72998000-73000000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr11:72998000-73000200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr11:72998200-72999600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr11:72998200-73000200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:72998200-73000200	Enhancers	Fetal Muscle Leg	muscle
27	chr11:72998200-73001000	Enhancers	Fetal Heart	heart
28	chr11:72998200-73001000	Enhancers	Left Ventricle	heart
29	chr11:72998400-72999800	Enhancers	Adipose Nuclei	Adipose
30	chr11:72998400-72999800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:72998400-73000200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:72998400-73000200	Enhancers	Fetal Muscle Trunk	muscle
33	chr11:72998400-73000200	Enhancers	Right Atrium	heart
34	chr11:72998400-73001200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr11:72998400-73003600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:72998600-72999600	Weak transcription	Brain Hippocampus Middle	brain
37	chr11:72998600-72999600	Bivalent Enhancer	HepG2	liver
38	chr11:72998600-73000800	Enhancers	Fetal Thymus	thymus
39	chr11:72998600-73000800	Enhancers	Right Ventricle	heart
40	chr11:72998600-73001000	Enhancers	Primary hematopoietic stem cells	blood
41	chr11:72998600-73001600	Enhancers	Primary B cells from cord blood	blood
42	chr11:72998600-73002000	Enhancers	Primary B cells from peripheral blood	blood
43	chr11:72998800-72999800	Enhancers	GM12878-XiMat	blood
44	chr11:72998800-72999800	Enhancers	Osteobl	bone
45	chr11:72998800-73000600	Enhancers	HSMMtube	muscle
46	chr11:72998800-73000800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:72998800-73001000	Enhancers	Stomach Mucosa	stomach
48	chr11:72998800-73001200	Enhancers	HUVEC	blood vessel
49	chr11:72999000-72999600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr11:72999000-72999800	Weak transcription	Brain Anterior Caudate	brain

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